[AMBER-Developers] prmtop file format specification/documentation

From: Timothy J Giese <timothyjgiese.gmail.com>
Date: Mon, 24 Oct 2011 19:19:24 -0400

I've been writing some code to read prmtop files.
I've been looking at http://ambermd.org/formats.html as my sole source
for the specification.

I have a few questions (for now).

(1) The specification suggests that %FLAG and %FORMAT are a part of the
specification, but some prmtop files in the amber distribution don't
have these. Are these not a part of the specification or are those
prmtop files malformed? Perhaps my reader should ignore these because
everybody else is?

(2) The %FLAG POINTERS section described in the specification suggests
that it should contain a list of 32 integers, but all the prmtop files
that I've found contain 31 integers.

(3) The pointer NUMEXTRA is described as "extra points found in the
topology"; however, the remainder of the documentation neglects to ever
again mention the words "NUMEXTRA" or "topology" - so it's unclear to me
what and where these extra points are. Do these affect the numbering of
all the atom index arrays - or perhaps how one of the sections is to be
read - or something else entirely? My only real concern here is
understanding how a non-zero value of NUMEXTRA effects the reading of
the numbers and how that changes the meaning of the numbers.

(4) %FLAG EXCLUDED_ATOMS_LIST suggests that INB is an array of atom
indices. This makes me believe that these are numbers from 1 to NATOM;
but I see that some prmtop files have values of "0". Is this a
c-offset/fortran-counting number issue or is there some undocumented
meaning to a value of 0?


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Received on Mon Oct 24 2011 - 16:30:02 PDT
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